Plugin 'Phenotypes' went wrong: Can't locate object method "transcript"

[michaeljon]

I'm trying to run the Phenotypes plugin, but adding the --offine option causes the following error. This is using a recent docker container with VEP 113. The Phenotypes.pm_homo_sapiens_113_GRCh38.gvf.gz database is downloaded and indexed. Taking --offline out of the command looks like it causes VEP to just hang.

vep -plugin Phenotypes,file=Phenotypes.pm_homo_sapiens_113_GRCh38.gvf.gz,include_types=Gene \
    --offline --force \
    --id "NC_000023.11       20582587        rs199695010     T       TC"

WARNING: Plugin 'Phenotypes' went wrong: Can't locate object method "transcript" via package "Bio::EnsEMBL::Variation::IntergenicVariationAllele" at /plugins/Phenotypes.pm line 328.

Running a stripped-down command does work.

vep \
    --cache --force --offline \
    --id "NC_000023.11       20582587        rs199695010     T       TC"

Edit -- The command does complete without --offline and fails with the same error.

[dglemos]

Hi @michaeljon, We are looking into this issue. Can you tell me from where you got the file Phenotypes.pm_homo_sapiens_113_GRCh38.gvf?

[michaeljon]

Thanks. I let the plugin download the files the first time it ran in --database mode.

vep
   --fork $(nproc) \
   --fasta GCF_000001405.40_GRCh38.p14_primary.fna \
   --use_given_ref \
   --species homo_sapiens \
   --output_file ./output.txt \
   --no_stats \
   --database \
   --assembly GRCh38 \
   --force \
   --vcf  \
   --merged \
   --plugin Phenotypes,file=/plugins/Phenotypes.pm_homo_sapiens_113_GRCh38.gvf.gz,include_types=Gene     \
   --format vcf \
   -i foo.vcf.gz

### Phenotypes plugin: Generating GFF file /plugins/Phenotypes.pm_homo_sapiens_113_GRCh38.gvf.gz from database
### Phenotypes plugin: This will take some time but it will only run once per species, assembly and release
### Phenotypes plugin: Querying database

[dglemos]

Thank you for providing the details. The issue with your job is that the plugin is attempting to fetch a transcript for an intergenic variant, which is causing the job to fail. We are working on a fix.

[dglemos]

We added a fix to the main branch. Can you please point your code to this branch and let me know if the issue is fixed?